Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/4d78c37285498e64014904e0b6f82f/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP_PON/pon.hotspot_protected.raw.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP_PON/pon.hotspot_protected.raw.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/4d78c37285498e64014904e0b6f82f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
==> STAGING COMPLETE (12 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i HCC1395_BL.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed --algo TNhaplotyper2 --tumor_sample HCC1395_BL --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz HCC1395_BL.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL HCC1395_BL.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments HCC1395_BL.tnseq_tumor_only.segments HCC1395_BL.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14381103, elapsed 0.1s, est remaining 1.9s, peak mem 148MB, user 0.6s, sys 0.0s, output queue size 55
progress 10% @chr21:25709334, elapsed 0.2s, est remaining 1.4s, peak mem 157MB, user 1.3s, sys 0.1s, output queue size 106
progress 15% @chr21:29027814, elapsed 0.2s, est remaining 1.1s, peak mem 163MB, user 1.8s, sys 0.1s, output queue size 22
progress 20% @chr21:30746851, elapsed 0.2s, est remaining 1.0s, peak mem 167MB, user 2.3s, sys 0.1s, output queue size 16
progress 25% @chr21:32354759, elapsed 0.3s, est remaining 0.9s, peak mem 172MB, user 3.0s, sys 0.1s, output queue size 63
progress 30% @chr21:33426784, elapsed 0.4s, est remaining 0.9s, peak mem 175MB, user 3.6s, sys 0.1s, output queue size 75
progress 35% @chr21:34379405, elapsed 0.4s, est remaining 0.8s, peak mem 178MB, user 4.2s, sys 0.2s, output queue size 74
progress 40% @chr21:33549376, elapsed 0.5s, est remaining 0.8s, peak mem 227MB, user 5.0s, sys 0.2s, output queue size 161
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progress 50% @chr21:39274274, elapsed 0.8s, est remaining 0.8s, peak mem 254MB, user 6.7s, sys 0.2s, output queue size 262
progress 55% @chr21:40178827, elapsed 0.9s, est remaining 0.7s, peak mem 266MB, user 7.4s, sys 0.2s, output queue size 369
progress 60% @chr21:41823218, elapsed 1.4s, est remaining 1.0s, peak mem 349MB, user 11.0s, sys 0.3s, output queue size 29
progress 65% @chr21:42382933, elapsed 1.7s, est remaining 0.9s, peak mem 366MB, user 13.1s, sys 0.4s, output queue size 112
progress 70% @chr21:43071885, elapsed 1.8s, est remaining 0.8s, peak mem 368MB, user 14.2s, sys 0.4s, output queue size 216
progress 75% @chr21:44119287, elapsed 1.8s, est remaining 0.6s, peak mem 374MB, user 14.9s, sys 0.4s, output queue size 327
progress 80% @chr21:44425570, elapsed 1.9s, est remaining 0.5s, peak mem 378MB, user 15.9s, sys 0.4s, output queue size 429
progress 85% @chr21:44906815, elapsed 2.0s, est remaining 0.4s, peak mem 378MB, user 16.7s, sys 0.5s, output queue size 503
progress 90% @chr21:46111377, elapsed 2.1s, est remaining 0.2s, peak mem 380MB, user 17.8s, sys 0.5s, output queue size 614
progress 95% @chr21:46322539, elapsed 2.2s, est remaining 0.1s, peak mem 381MB, user 19.3s, sys 0.5s, output queue size 70
progress 100% @chr21:46661700, elapsed 2.3s, est remaining 0.0s, peak mem 381MB, user 20.3s, sys 0.5s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050657
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 12 max 96
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 163002590
output file size: 51811
reads: 1955548
contig: 1979 intervals 801713 bases
"assemble": 227 calls 0.933 user 0.030 sys 0.970 real
"assemble_addRead": 227 calls 0.020 user 0.000 sys 0.023 real
"assemble_buildGraph": 511 calls 0.407 user 0.010 sys 0.443 real
"assemble_computecigar": 321 calls 0.135 user 0.020 sys 0.152 real
"assemble_kg_build_calcsize": 511 calls 0.181 user 0.000 sys 0.240 real
"assemble_kg_build_clear": 699 calls 0.047 user 0.000 sys 0.024 real
"assemble_kg_build_prepare": 1022 calls 0.201 user 0.020 sys 0.234 real
"assemble_kg_build_threading": 323 calls 0.189 user 0.010 sys 0.189 real
"assemble_kg_op1": 323 calls 0.130 user 0.000 sys 0.125 real
"assemble_kg_op2": 323 calls 0.020 user 0.000 sys 0.006 real
"assemble_kg_op3": 323 calls 0.000 user 0.000 sys 0.007 real
"assemble_sg_clean": 321 calls 0.035 user 0.000 sys 0.036 real
"assemble_sg_create": 321 calls 0.090 user 0.000 sys 0.052 real
"checkGraph": 227 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 227 calls 0.135 user 0.020 sys 0.158 real
advance: 2074 calls 6.957 user 0.210 sys 7.296 real
assemble_region: 227 calls 1.088 user 0.050 sys 1.154 real
build_pileup: 1957 calls 0.060 user 0.000 sys 0.059 real
build_stats: 1979 calls 1.733 user 0.081 sys 1.846 real
build_variants: 179 calls 0.000 user 0.000 sys 0.001 real
calc: 3869 calls 0.989 user 0.000 sys 0.940 real
calc_region: 179 calls 5.233 user 0.021 sys 5.321 real
call_region: 179 calls 0.080 user 0.000 sys 0.089 real
clip_region: 406 calls 0.020 user 0.000 sys 0.071 real
done: 1 calls 0.700 user 0.000 sys 0.701 real
execute: 1 calls 0.009 user 0.001 sys 2.291 real
fetch: 8147 calls 1.180 user 0.001 sys 1.284 real
fetch_ref: 8428 calls 0.021 user 0.000 sys 0.061 real
fetch_region: 227 calls 0.040 user 0.000 sys 0.022 real
fetch_vcf: 2074 calls 0.712 user 0.012 sys 0.839 real
idle: 42 calls 0.076 user 0.000 sys 13.259 real
init: 1 calls 0.060 user 0.010 sys 0.078 real
pairhmm: 1058 calls 10.129 user 0.031 sys 10.042 real
realign: 179 calls 0.699 user 0.000 sys 0.774 real
region: 4053 calls 6.393 user 0.072 sys 6.535 real
tracker: 4053 calls 0.030 user 0.000 sys 0.016 real
trim_region: 227 calls 0.000 user 0.000 sys 0.003 real
overall: 400363520 mem 27.543 user 0.609 sys 3.612 real